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celltype and broad celltype count¶

     B cell progenitor        CD14+ Monocytes        CD16+ Monocytes 
                   522                   3369                    461 
            CD4 Memory              CD4 Naive           CD8 effector 
                  2227                   1952                    755 
             CD8 Naive         Dendritic cell Double negative T cell 
                  1297                    133                    147 
               NK cell                    pDC              Platelets 
                   477                    114                      2 
            pre-B cell 
                   453 
 Lymphoid   Myeloid Platelets 
     8077      3830         2 
     B cell progenitor        CD14+ Monocytes        CD16+ Monocytes 
                   636                   4032                    506 
            CD4 Memory              CD4 Naive           CD8 effector 
                  1999                   1549                    747 
             CD8 Naive         Dendritic cell Double negative T cell 
                  1069                    131                    138 
               NK cell                    pDC              Platelets 
                   458                    126                      5 
            pre-B cell 
                   620 
 Lymphoid   Myeloid Platelets 
     7473      4538         5 
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.10.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] psych_2.0.9         magrittr_1.5        ggbio_1.38.0       
 [4] BiocGenerics_0.36.0 msigdbr_7.2.1       ggpubr_0.4.0       
 [7] Signac_1.0.0        Seurat_3.2.2        reticulate_1.16    
[10] purrr_0.3.4         data.table_1.13.2   cowplot_1.1.0      
[13] ggplot2_3.3.2       MOFA2_0.99.6       

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1              SnowballC_0.7.0            
  [3] rtracklayer_1.50.0          pbdZMQ_0.3-4               
  [5] GGally_2.0.0                tidyr_1.1.2                
  [7] bit64_4.0.5                 knitr_1.30                 
  [9] irlba_2.3.3                 DelayedArray_0.16.0        
 [11] rpart_4.1-15                RCurl_1.98-1.2             
 [13] AnnotationFilter_1.14.0     generics_0.0.2             
 [15] GenomicFeatures_1.42.0      RSQLite_2.2.1              
 [17] RANN_2.6.1                  future_1.20.1              
 [19] bit_4.0.4                   spatstat.data_1.4-3        
 [21] xml2_1.3.2                  httpuv_1.5.4               
 [23] SummarizedExperiment_1.20.0 assertthat_0.2.1           
 [25] xfun_0.18                   hms_0.5.3                  
 [27] evaluate_0.14               promises_1.1.1             
 [29] progress_1.2.2              readxl_1.3.1               
 [31] dbplyr_2.0.0                tmvnsim_1.0-2              
 [33] igraph_1.2.6                DBI_1.1.0                  
 [35] htmlwidgets_1.5.2           reshape_0.8.8              
 [37] stats4_4.0.3                ellipsis_0.3.1             
 [39] RSpectra_0.16-0             corrplot_0.84              
 [41] dplyr_1.0.2                 backports_1.1.10           
 [43] biomaRt_2.46.0              deldir_0.2-2               
 [45] MatrixGenerics_1.2.0        vctrs_0.3.4                
 [47] Biobase_2.50.0              Cairo_1.5-12.2             
 [49] ensembldb_2.14.0            ROCR_1.0-11                
 [51] abind_1.4-5                 withr_2.3.0                
 [53] BSgenome_1.58.0             checkmate_2.0.0            
 [55] sctransform_0.3.1           GenomicAlignments_1.26.0   
 [57] prettyunits_1.1.1           mnormt_2.0.2               
 [59] goftest_1.2-2               cluster_2.1.0              
 [61] IRdisplay_0.7.0             lazyeval_0.2.2             
 [63] crayon_1.3.4                labeling_0.3               
 [65] pkgconfig_2.0.3             GenomeInfoDb_1.26.0        
 [67] nlme_3.1-149                vipor_0.4.5                
 [69] ProtGenerics_1.22.0         nnet_7.3-14                
 [71] rlang_0.4.8                 globals_0.13.1             
 [73] lifecycle_0.2.0             miniUI_0.1.1.1             
 [75] BiocFileCache_1.14.0        rsvd_1.0.3                 
 [77] dichromat_2.0-0             cellranger_1.1.0           
 [79] ggrastr_0.2.1               polyclip_1.10-0            
 [81] matrixStats_0.57.0          lmtest_0.9-38              
 [83] graph_1.68.0                Matrix_1.2-18              
 [85] ggseqlogo_0.1               IRkernel_1.1.1.9000        
 [87] carData_3.0-4               Rhdf5lib_1.10.1            
 [89] zoo_1.8-8                   base64enc_0.1-3            
 [91] beeswarm_0.2.3              ggridges_0.5.2             
 [93] pheatmap_1.0.12             png_0.1-7                  
 [95] viridisLite_0.3.0           bitops_1.0-6               
 [97] KernSmooth_2.23-17          Biostrings_2.58.0          
 [99] blob_1.2.1                  stringr_1.4.0              
[101] qvalue_2.22.0               parallelly_1.21.0          
[103] jpeg_0.1-8.1                rstatix_0.6.0              
[105] S4Vectors_0.28.0            ggsignif_0.6.0             
[107] scales_1.1.1                memoise_1.1.0              
[109] plyr_1.8.6                  ica_1.0-2                  
[111] zlibbioc_1.36.0             compiler_4.0.3             
[113] RColorBrewer_1.1-2          fitdistrplus_1.1-1         
[115] Rsamtools_2.6.0             XVector_0.30.0             
[117] listenv_0.8.0               patchwork_1.0.1            
[119] pbapply_1.4-3               htmlTable_2.1.0            
[121] Formula_1.2-4               MASS_7.3-53                
[123] mgcv_1.8-33                 tidyselect_1.1.0           
[125] stringi_1.5.3               forcats_0.5.0              
[127] askpass_1.1                 latticeExtra_0.6-29        
[129] ggrepel_0.8.2               grid_4.0.3                 
[131] VariantAnnotation_1.36.0    fastmatch_1.1-0            
[133] tools_4.0.3                 future.apply_1.6.0         
[135] rio_0.5.16                  rstudioapi_0.11            
[137] uuid_0.1-4                  foreign_0.8-80             
[139] lsa_0.73.2                  gridExtra_2.3              
[141] farver_2.0.3                Rtsne_0.15                 
[143] digest_0.6.25               BiocManager_1.30.10        
[145] shiny_1.5.0                 Rcpp_1.0.5                 
[147] GenomicRanges_1.42.0        car_3.0-10                 
[149] broom_0.7.2                 later_1.1.0.1              
[151] RcppAnnoy_0.0.16            OrganismDbi_1.32.0         
[153] httr_1.4.2                  AnnotationDbi_1.52.0       
[155] biovizBase_1.38.0           colorspace_1.4-1           
[157] XML_3.99-0.5                tensor_1.5                 
[159] IRanges_2.24.0              splines_4.0.3              
[161] uwot_0.1.8                  RBGL_1.66.0                
[163] RcppRoll_0.3.0              spatstat.utils_1.17-0      
[165] plotly_4.9.2.1              xtable_1.8-4               
[167] jsonlite_1.7.1              spatstat_1.64-1            
[169] R6_2.4.1                    Hmisc_4.4-1                
[171] pillar_1.4.6                htmltools_0.5.0            
[173] mime_0.9                    glue_1.4.2                 
[175] fastmap_1.0.1               BiocParallel_1.24.0        
[177] codetools_0.2-16            lattice_0.20-41            
[179] tibble_3.0.4                curl_4.3                   
[181] ggbeeswarm_0.6.0            leiden_0.3.4               
[183] zip_2.1.1                   openxlsx_4.2.3             
[185] openssl_1.4.3               survival_3.2-7             
[187] repr_1.1.0                  munsell_0.5.0              
[189] rhdf5_2.32.4                GenomeInfoDbData_1.2.4     
[191] HDF5Array_1.16.1            haven_2.3.1                
[193] reshape2_1.4.4              gtable_0.3.0